This post is intended to act as a brief Situation Report (SITREP) about the concerning
developments regarding a new strain of SARS-CoV-2 -
the virus that is causing the COVID-19 global pandemic.
The data presented was gratefully sourced from GISAID.
As of 01/18/2021, there's been 17878 sequences
detected in over 38 countries under this strain (see table for definition).
In the US, there's been 86 sequences detected in over 15 states.
This report follows a bottom-up approach starting with background information, and followed by
prevalence at the state, national, and global level in that order.
The table on the left contains the key mutations that represent the strain. The plot on the
right compares the genetic distance, a measure of evolutionary progress, between B117
and non-B117 (related) samples.
| Gene | Nucleotide Mutations | Amino Acid Changes |
|---|---|---|
| ORF1ab | C3266T, T6953C, C5387A, 11288:11296 deletion | T1001I, I2230T, A1708D |
| S | A23062T, C23270A, A23402G, C23603A, C23708T, T24505G, G24913C | DEL69-70, DEL144Y, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H |
| N | GAT28279CTA, C28976T | D3L, S235F |
| ORF8 | G28047T, C27971T, A28110G | R52I, Q27_, Y73C |
As figure 3.2 indicates, the B.1.1.7 genomes in the US (so far),
were not a result of unbiased sequencing but were identified by S-gene
target failures (SGTF) in community-based diagnostic PCR testing. Since
it was not an unbiased approach, it does not indicate the true prevalence
of the B117 lineage in the US. This only tells us that the lineage is
present in the US.
P.S: estimates of true prevalence in the US are discussed in
this post